Molecular mechanisms Flashcards
1
Q
What is the function of micro RNA (miRNA)?
A
Master regulator of gene function
2
Q
What is RNA interference (RNAi)?
A
Post-transcriptional regulation by small interfering RNAs
3
Q
In which organism were miRNA & RNAi discovered?
A
C. elegans
4
Q
How is miRNA encoded into the genome?
A
In non-protein coding genes
5
Q
How long are miRNA gene transcripts?
A
<200 nucleotides
6
Q
What is the most important processor of unprocessed miRNA gene transcripts? What is its function?
A
DICER -> cuts pre-miRNA into smaller structures, ~20-22bp
7
Q
What is the length of processed miRNA?
A
20-22 nucleotides
8
Q
What happens when miRNA has been fully processed?
A
They associate with the RISC-complex
9
Q
Which two structures make up the RISC complex?
A
- DICER
- Argonaut
10
Q
What is the function of the RISC complex? What is the role in miRNA in the RISC complex?
A
The RISC complex interferes with mRNA and uses miRNA to recognize specific mRNA transcripts
11
Q
What happens when there is perfect complementarity between RISC-associated miRNA and mRNA?
A
mRNA is completely degraded by DICER
12
Q
What happens when there is partial complementarity between RISC-associated miRNA and mRNA?
A
RISC-complex associates with mRNA and blocks translation
13
Q
How many % of mammalian DNA is regulated by miRNA?
A
60%
14
Q
In which processes (among others) does miRNA regulation play a vital role? (3)
A
- Embryonic development
- Cancer (dysregulation)
- Other diseases
15
Q
What is the main function of RNA interference (RNAi) in plants and invertebrates?
A
Forms a protection against viruses by recognizing dsRNA viral RNA and destroying it
16
Q
How can invertebrates & plants build up immunological memory, despite their lack of an adaptive immune system?
A
They can incorporate viral transcripts into genome, using them to form miRNAs that can help the RISC-complex recognize and destroy invading virus RNA
17
Q
Why are mammalian cells not reliant on RNAi for antiviral defence?
A
Mammals have potent antiviral IFN responses
18
Q
In which two ways can miRNA be coded into the genome?
A
- Coding for a single pri-miRNA
- Polycistronic -> larger transcript, coding for multiple pri-miRNAs
19
Q
What is pri-miRNA?
A
miRNA transcript before processing by DICER
20
Q
By which three ways can miRNA-RISC complexes modify mRNA translation?
A
- Blocking translation of target mRNA
- Degrading target mRNA
- Deadenylate target mRNA
21
Q
Which finding gives rise to the theory that miRNA has a broad function in immune regulation?
A
The fact that every immune cell type has a characteristic miRNA profile
22
Q
What is the predominant miRNA in the liver?
A
miR-122
23
Q
In which liver processes is miR-122 involved? (3)
A
- Metabolism, specifically lipid homeostasis
- Stress responses
- Preventing cancer development
24
Q
Which virus is reliant upon the presence of miR-122 for replication?
A
HCV
25
What is misregulation of miR-122 associated with?
Hepatocellular carcinoma
26
For which processes is HCV reliant on miR-122? (2)
1. miR-122 binds to an untranslated region of the HCV viral +RNA and boosts translation
2. HCV -RNA has miR-122 docking stations -> miR-122 binding leads to genome stability, more translation of viral protein & genome replication
27
Where does HCV enter the hepatocyte?
Tight junction
28
What is the effect of miR-122 docking to HCV -RNA? (3)
1. Genome stability
2. Stuctural alteration of the genome -> translation of more viral protein
3. Genome replication & translation-replication switch
29
What is a possible therapeutic application of miRNA?
Targeting/mimicking miRNA with antisense oligonucleotides (ASO)
30
What are LNA-molecules? What is their function?
LNA = locked nucleic acid = synthetic modified DNA, resistant to degradation
Function: silencing miRNA
31
How long does the effect of antisense oligonucleotides aimed at miR-122 last?
60-80 days
32
What are the effects of antisense oligonucleotides aimed at miR-122 in HCV? (2)
1. Reduction of plasma cholesterol (side effect)
2. Dose-dependent, gradual decrease of HCV RNA levels
33
Why is antisense oligonucleotide therapy aimed at miR-122 not routinely used?
Antivirals for HCV make this treatment redundant
34
How can miRNAs be tranported through the body? What effect would this have?
Exosomes/microvesicles -> transport would allow miRNAs to modify the behaviour of other cells
35
In which forms can miRNA be released when a cell dies? (3)
1. Part of apoptotic bodies
2. Free RISC-miRNA complexes
3. Free miRNA
36
How are miRNAs from food hypothesized to influence human gene translation?
If food-derived miRNAs can survive the harsh environment of the gastrointestinal tract, they could possibly modify human gene translation
37
Where do ingested miRNAs accumulate?
The liver
38
What is the benefit of using miRNAs as a biomarker? (4)
1. miRNAs are master regulators of gene biological processes
2. Easy & sensitive detection of miRNAs is possible
3. Highly stable & insensitive to degradation
4. Highly cell-type specific expression patterns
39
Why is miR-122 a good biomarker for liver injury? (2)
1. More sensitive to liver damage than ALAT
2. miR-122 increases much faster after liver damage occurs (near-instant vs. ~24 hours)
40
What shows that miR-122 is a more sensitive marker of liver damage than ALAT?
ALAT is not elevated in chronic HCV patients, but miR-122 is
41
What are the applications of miRNA diagnostics in liver transplantation? (2)
1. Assessment of liver quality prior to Tx
2. Detection of rejection/damage post-Tx
42
What is the overall purpose of DNA repair?
Maintaining integrity of genetic material
43
Which DNA repair pathways are there? (6)
1. Base excision repair (BER)
2. Mismatch repair (MMR)
3. Nucleotide excision repair (NER)
4. Non-homologous end-joining (NHEJ)
5. Alternative end-joining (AEJ)
6. Homologous recombination (HR)
44
What determines which DNA repair pathway is used?
The type of DNA damage
45
Which forms of DNA damage are repaired by base excision repair (BER)? (4)
1. Oxidation
2. Uracil
3. Abasic site
4. Single strand break
46
Which agents can cause the types of DNA damage repaired by base excision repair? (4)
1. ROS
2. X-rays
3. Alkylating agents
4. Spontaneous reactions
47
Which forms of DNA damage are repaired by mismatch repair (MMR)? (4)
1. A-G mismatch
2. T-C mismatch
3. Insertion
4. Deletion
48
What causes the types of DNA damage repaired by mismatch repair (MMR)?
Replication errors
49
Which forms of DNA damage are repaired by nucleotide excision repair (NER)? (2)
1. Bulky adducts
2. Intrastrand crosslinks
50
What causes the types of DNA damage repaired by nucleotide excision repair (NER)? (2)
1. UV-light
2. Polycyclic aromatic hydrocarbons
51
Which mechanisms are responsible for the repair of double-strand DNA breaks (dsDNA breaks)? (3)
1. Non-homologous end-joining (NHEJ)
2. Homologous recombination (HR)
3. Alternative end-joining (AEJ)
52
Which types of damage can cause dsDNA breaks? (3)
1. X-rays
2. Ionizing radiation
3. Anti-tumour agents
53
For which immunological cells is DNA repair especially crucial?
Lymphocytes -> rely on DNA breaks & repair to generate a diverse receptor repertoire
54
Which processes of B- and/or T-cells rely on DNA repair?
1. V(D)J-recombinatin -> both B- and T-cells
2. Somatic hypermutation (SHM) -> B-cells
3. Class switch recombination (CSR) -> B-cells
55
Which DNA repair mechanisms is responsible for V(D)J recombination?
Non-homologous end-joining (NHEJ)
56
Where does V(D)J-recombination of T-cells take place?
Thymus
57
Where does V(D)J-recombination of B-cells take place?
Bone marrow
58
When does somatic hypermutation (SHM) of B-cells take place?
Germinal centre reaction
59
Which DNA repair mechanisms are involved in somatic hypermutation (SHM)? (2)
1. Mismatch repair (MMR)
2. Base-excision repair (BER)
60
Which DNA repair mechanisms are involved in class switch recombination (CSR)? (3)
1. Non-homologous end-joining (NHEJ)
2. Base-excision repair (BER)
3. Alternative end-joining (AEJ)
61
Where does class switch recombination (CSR) of B-cells take place?
Germinal centre reaction
62
What is the purpose of V(D)J-recombination?
Achieving combinatorial diversity to expand the receptor repertoire
63
What is the process of V(D)J-recombination to final receptor transcript? (4)
1. D- to J-rearrangement (only heavy chain)
2. V- to (D)J rearrangement
3. Transcription
4. Splicing to obtain final transcript
64
Which mechanisms add extra diversity during V(D)J-recombination? (2)
1. p-nucleotide addition
2. n-nucleotide addition
65
What is the process of DNA breakage & joining in V(D)J-recombination? (4)
1. RAG1 & RAG2 form heterodimer to cut DNA
2. RAG-complex recognizes conserved recombination signal sequences (RSS) and makes cuts here
3. RAG makes hairpin in DNA to connect complementary strands
4. Non-homologous recombination of the two strands: Artemis opens hairpin & DNA ligase ligates strands
66
Which part of the DNA breakage & joining in V(D)J-recombination is specific?
The initiation of DNA breaks by RAG
67
In which cell types is RAG expressed?
Tightly regulated to lymphocyte progenitors
68
Why is RAG expression tightly regulated?
Unwarranted expression could cause DNA breaks when this is unwanted
69
When is unwarranted expression of RAG especially dangerous?
During cell division
70
Where can recombination signal sequences (RSSs) be found?
In the flanking regions of V-, D- and J-genes
71
Why is it necessary that the RAG complex makes a hairpin after creating a dsDNA break?
To leave behind no reactive DNA damage that can further damage the DNA
72
What is the process of hairpin opening by Artemis during NHEJ? (3)
1. Broken ends are recognized by KU-enzymes
2. KU recruits DNA-PKcs
3. DNA-PKcs recruits Artemis -> cleaves open hairpins
73
Which enzymes are involved in strand ligation after hairpin opening by Artemis in NHEJ? (3)
1. DNA ligase 4
2. XLF
3. XRCC4
74
Which enzyme is responsible for n-nucleotide addition during V(D)J-recombination?
Tdt
75
When does Tdt add n-nucleotides?
Just before DNA-ligation during the NHEJ step of V(D)J-recombination
76
What is the effect of a complete V(D)J-recombination defect?
SCID
77
What is the presentation of SCID? (6)
1. Early onset (<3 months of age)
2. Repeated, severe & opportunistic infections
3. Failure to thrive
4. Chronic diarrhoea due to gastro-enteritis
5. Lymphocytopenia
6. Hypo-/agammaglobulinaemia
78
Which to types of T-B- SCID can be identified?
1. Non-radiosensitive T-B- SCID
2. Radiosensitive T-B- SCID
79
What is the cause of non-radiosensitive SCID?
Defect in lymphoid-specific DNA break initiation due to RAG1/RAG2 mutations
80
What is the cause of radiosensitive SCID?
Defect in NHEJ machinery
81
What is the effect of the defect in NHEJ machinery in radiosensitive SCID?
All body cells are sensitive to ionizing radiation
82
How is radiosensitivity tested in SCID patients?
Exposing patient skin fibroblasts to ionizing radiation
83
Why is it important to test SCID patients for radiosensitivity? (2)
1. Non-radiosensitive SCID can be cured using HSCT, for which radiation & cell-killing agents are used -> dangerous for patients unable to perform DNA repair
2. Non-immune cell defects will not be restored by HSCT
84
Which gene defects are no. 1 and 2 for causing T-B- SCID?
Majority = RAG
2nd = Artemis
85
What makes SCID exceedingly rare?
All genes involved in V(D)J-recombination are located on autosomal genes and rarely have a complete dysfunction
86
In addition to radiosensitivity, what do radiosensitive SCID patients suffer from? (3)
1. Severe imunodeficiency
2. Neurological abnormalities
3. Other abnormalities such as primordial dwarfism
87
What makes that the neurological & immunological consequences of SCID occur along a spectrum of severity?
Residual enzyme function may somewhat reduce severity
88
What is a frequently seen neurological abnormality in SCID patients?
Microcephaly
89
What is an important prerequisite for good dsDNA break repair?
The strands of the break need to be held together until they can be ligated
90
What are the steps of the process of holding DNA strands together in case of a dsDNA break? (3)
1. MRN-complex formation -> holds ends together
2. ATM-docking -> signalling hub for DNA damage
3. Initiation of repair & shutdown of cell proliferation until damage is repaired
91
Which factors make up the MRN complex, responsible for holding the strands of dsDNA breaks together? (3)
1. MRE11
2. RAD50
3. NBN = Nibrin
92
Which factors dock to the ATM DNA damage signalling hub? (2) Why is this useful knowledge?
1. MDC1
2. 53BP1
Antibodies against 53BP1 can be used to show unrepaired DNA ends
93
What is Nijmegen Breakage syndrome?
Impaired DNA damage responses due to a biallelic mutation in the NBN gene
94
What are the characteristics of Nijmegen Breakage syndrome? (7)
1. Chromosomal instability
2. Bird-like face
3. Microcephaly
4. Growth retardation
5. Strong predisposition to malignancies
6. Immunodeficiency due to lymphopenia
7. Strong sensitivity to ionizing radiation
95
What is the result of the NBN mutation in Nijmegen Breakage syndrome for V(D)J-recombination?
Loss of juxtapostion of RAG-induced breaks -> results in inefficient B-cell development
96
Which stages of B-cell maturation make up the majority of the B-cell component in Nijmegen Breakage syndrome patients? (2) Which components are low? (2)
High:
1. Pro-B
2. Pre-BI
Low:
1. Pre-BII
2. Immature B-cells
97
Why are there still some immature B-cells in Nijmegen Breakage syndrome patients?
Loss of juxtaposition of RAG-induced breaks severely reduces recombination efficiency, but does not block it
98
What is ataxia telangiectasia?
Chromosomal instability syndrome due to biallelic mutations in ATM gene
99
What are the characteristics of ataxia telangiectasia? (5)
1. Cerebellar deteroriation/ataxia
2. Telangiectasia
3. Strong predisposition to malignancies
4. Variable immunodeficiency
5. Severe sensitivity to ionizing radiation
100
To what kind of infection are ataxtia telangiectasia patients especially sensitive?
Bacterial infection
101
How is hypogammaglobulinaemia in ataxia telangiectasia patients treated?
IVIG
102
What are the two processes of the germinal centre response? Which is first? Where do they take place?
First: somatic hypermutation in the dark zone of the germinal centre
Second: class switch recombination in the light zone of the germinal centre
103
How is somatic hypermutation performed?
Random mutations are added to the variable domain of the BCR
104
What is required to initiate somatic hypermutation?
T-cell help
105
Where is the majority of mutations in somatic hypermutation concentrated?
The complementarity determining regions of the variable domain of the BCR
106
What happens when antigen-binding after somatic hypermutation is disrupted?
No antigen-internalization & presentation to T-cells -> no T-cell help -> apoptosis
107
What happens when antigen-binding after somatic hypermutation is retained/increased?
Internalization & antigen -> presentation of MHCII -> T-cell help -> survival
108
Into which cell types can B-cells differentiate after somatic hypermutation? (2)
1. Plasmablast -> plasma cell
2. Memory cell
109
What happens during class switch recombination?
The constant domain of the antibody is replaced by that of another isotype
110
What initiates class switch recombination, and determines the new isotype?
Presence of cytokines during the germinal centre reaction
111
What is the most commonly used new isotype for B-cells in class switch recombination?
IgG1
112
Which constant regions can be found in the BCR of naïve B-cells? What are their isotypes?
Cμ and Cδ, resulting in IgM and IgD
113
What determines whether a naïve B-cell BCR is an IgM or IgD subtype?
Alternative splicing
114
What is the switch region of the BCR?
The gene region to which new isotypes can be coupled
115
To which constant domains (&isotypes) can B-cells switch during class switch recombination?
Cγ 1/2/3/4 -> IgG1/2/3/4
Cα 1/2 /-> IgA1/2
Cε -> IgE
116
What are somatic hypermutation & class switch recombination both dependent on?
AID-dependent lesions
117
What is AID? What does it do?
Activation-induced cytidine deaminase -> deaminates cytidines, turning them into uracil -> causes mismatch
118
What is the concentration of AID-dependent lesions in somatic hypermutation? What does this result in?
Low concentration of lesions, resulting in point mutations which are randomly repaired -> causes mutations
119
What is the concentration of AID-dependent lesions in class switch recombination? What does this result in?
High amount of AID target sites causes high accumulation of lesions -> dsDNA breaks
120
How are low-density AID-dependent laesions repaired in somatic hypermutation? (3) What do they each result in?
1. No repair -> DNA gets repaired uring next proliferation, where U gets seen as T. Result: CG-base-pair transitions into A-T
2. Base-excision repair -> abasic site gets removed, a random nucleotide can be moved in.
Result: mostly repaired with a C, but can also be other nucleotides.
3. Mismatch repair -> whole stretch of DNA removed & reconstructed based on the complementary strand.
Result: MMR = error-prone -> frequent introduction of mutations
121
What allows AID-induced dsDNA breaks in class switch recombination to be repaired by NHEJ?
Switch regions of BCR genes have high homology -> allows for switch using alternative isotypes
122
Which disease is an example of a disease that results from a defect in class switch recombination?
Hyper-IgM syndrome
123
What causes hyper-IgM syndrome? What is its mechanism?
UNG deficiency
UNG = necessary to excise U in BER -> causes defect in class switch recombination
124
What are the characteristics of hyper-IgM syndrome? (3)
1. Patients are susceptible to bacterial infections
2. Normal/increased IgM
3. Low/absent IgG, IgE & IgA
125
What is an additional problem of the antibodies in hyper-IgM syndrome?
Impaired affinity maturation -> low affinity antibodies
